Atomic-scale fabrication is an effective way to realize the ultra-smooth surfaces of semiconductor wafers on an atomic scale. As one of the crucial manufacturing means for atomically precise surface of large-sized functional materials, chemical mechanical polishing (CMP) has become a key technology for ultra-smooth and non-damage surface planarization of advanced materials and devices by virtue of the synergetic effect of chemical corrosion and mechanical grinding. It has been widely used in aviation, aerospace, microelectronics, and many other fields. However, in order to achieve ultra-smooth surface processing at an atomic level, chemical corrosion and mechanical grinding methods commonly used in CMP process require some highly corrosive and toxic hazardous chemicals, which would cause irreversible damage to the ecosystems. Therefore, the recently reported green chemical additives used in high-performance and environmentally friendly CMP slurry for processing atomically precise surface are summarized here in this paper. Moreover, the mechanism of chemical reagents to the modulation of materials surface properties in the CMP process is also analyzed in detail. This will provide a reference for improving the surface characteristics on an atomic scale. Finally, the challenges that the polishing slurry is facing in the research of atomic-scale processing are put forward, and their future development directions are prospected too, which has profound practical significance for further improving the atomic-scale surface accuracy.